IODS course project
Anne Tyvijärvi
Introduction to Open Data Science - Course Project
How are you feeling right now? What do you expect to learn? Where did you hear about the course?
- I feel like
- I’m going to learn a lot
- I might need some help along the way
- A friend of mine
- told me about the course and
- encouraged me to participate
Also reflect on your learning experiences with the R for Health Data Science book and the Exercise Set 1: How did it work as a “crash course” on modern R tools and using RStudio? Which were your favorite topics? Which topics were most difficult? Some other comments on the book and our new approach of getting started with R Markdown etc.?
- The book is really nice because
- the examples are clear and well explained
- In addition
- for me, it really helps to have the code ready and to be able to try them for myself while reading
- nothing has been “difficult”, although there were many things that I’ve never seen or tried before
## [1] "The date today is"##
## Attaching package: 'lubridate'## The following objects are masked from 'package:base':
##
## date, intersect, setdiff, union## [1] "2023-11-20 15:47:09 EET"The text does not continue here
Assignment 2: Data wrangling and analysis
Anne Tyvijärvi
The learning2014 data is based on the international survey of Approaches to Learning. Observations with “zero” value for exam points have been removed from the data. “Deep”, “stra” and “surf” are combination variables (averages) of individual measurements measuring the same “dimension”.The data frame includes 166 rows and 7 columns, and all data (except gender that is “character”) is numeric.
With the function plot() you can see that the majority of participants identified as female, and most participants were 20 - 30 years. There was a strong positive correlation between attitude and exam points (p < 0.001), and a negative correlation between deep learning (questions related to measuring the understanding of what is being studied) and attitude (p < 0.05), but also deep learning and learning strategy (making an effort to learn).
Based on the above results, I chose attitude, deep (relating to the “depth” of learning) and stra (learning strategies) as explanatory varibles for exam points, and tested these with the linear regression: + Model fit: The distribution of residuals not symmetrically distributed across 0, thus model fit is not necessarily good
t-value for points and attitude is 6.203, which indicates a possible relationship between the two variables. This is also indicated in the coefficient column (PR(>t)), where p < 0.001
t-value for deep and stra is close to zero, so likely there is no relationship between points and deep/stra (although p < 0.1 for stra, so there might be a tendency of learning strategies having a relationship with exam points)
R2 for the model is 0.2097, so 20.97% of the variance of the response variable (points) could be explained by the predictor variables (attitude, deep and stra)
Based on the above, the variables deep and stra were removed from the next regression analysis (See below for results).
Model fit: The distribution of residuals more symmetrical than when the other two variables were included in the model => better fit
t-value for attitude is 6.124 and p < 0.001, indicating a strong relationship between exam points and attitude
R2 (multiple R squared) is 0.1906, so 19.06% of the variance in points was explained by attitude alone
Next, I tested if the model meets the assumptions of linear regression (i.e., linearity, independence, homoscedasticity, normality, no multicolinearity and no endogeneity). The “Residuals vs.fitted” plot can be used to detect non-linearity, unequal error variances, and outliers.In our data, 145, 56 and 35 seem to be outliers (but other than that the residuals are quite evenly distributed around 0). The “Q-Q Residuals” plot is used to check for normality of residuals. Here you can also see the outliers of our data. The “Residuals vs. Leverage” can be used to check for homoscedasticity and non-linearity. With our data, the spread of standardized variables increases as a function of leverage, indicating heteroscedasticity. Based on these results I would either remove outliers from the data or try data transformations (log10, square root..) to meet the assumptions of the linear regression model.
library(GGally)## Warning: package 'GGally' was built under R version 4.3.2## Loading required package: ggplot2## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2library(ggplot2)
library(tidyverse)## Warning: package 'tidyverse' was built under R version 4.3.2## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.3 ✔ stringr 1.5.0
## ✔ forcats 1.0.0 ✔ tibble 3.2.1
## ✔ purrr 1.0.2 ✔ tidyr 1.3.0
## ✔ readr 2.1.4## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(readr)
#Set the working directory and read the data into R
setwd("C:/Users/03114911/OneDrive - Valtion/Anne's PhD papers, results, plans etc/MBDP/Open data science/IODS-project")
learning2014_readback <- read_csv("Data/learning2014.csv", show_col_types = FALSE)
#Data structure and dimensions: these allow you to learn basic information of your data
str(learning2014_readback) # all data is numeric, except gender is "character"("M"/"F")## spc_tbl_ [166 × 7] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
## $ gender : chr [1:166] "F" "M" "F" "M" ...
## $ age : num [1:166] 53 55 49 53 49 38 50 37 37 42 ...
## $ attitude: num [1:166] 3.7 3.1 2.5 3.5 3.7 3.8 3.5 2.9 3.8 2.1 ...
## $ deep : num [1:166] 3.58 2.92 3.5 3.5 3.67 ...
## $ stra : num [1:166] 3.38 2.75 3.62 3.12 3.62 ...
## $ surf : num [1:166] 2.58 3.17 2.25 2.25 2.83 ...
## $ points : num [1:166] 25 12 24 10 22 21 21 31 24 26 ...
## - attr(*, "spec")=
## .. cols(
## .. gender = col_character(),
## .. age = col_double(),
## .. attitude = col_double(),
## .. deep = col_double(),
## .. stra = col_double(),
## .. surf = col_double(),
## .. points = col_double()
## .. )
## - attr(*, "problems")=<externalptr>dim(learning2014_readback) # the data has 166 rows and 7 columns## [1] 166 7#Plot the relationships between variables in learning2014_readback to see how the variables are related and if there are any significant relationships. Alpha set to 0.1, only showing significance p > 0.1.
plot <- ggpairs(learning2014_readback, mapping = aes(col = gender, alpha = 0.1))
plot## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
# Multiple regression
model1 <- lm(points ~ attitude + deep + stra, data = learning2014_readback)
summary(model1)##
## Call:
## lm(formula = points ~ attitude + deep + stra, data = learning2014_readback)
##
## Residuals:
## Min 1Q Median 3Q Max
## -17.5239 -3.4276 0.5474 3.8220 11.5112
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 11.3915 3.4077 3.343 0.00103 **
## attitude 3.5254 0.5683 6.203 4.44e-09 ***
## deep -0.7492 0.7507 -0.998 0.31974
## stra 0.9621 0.5367 1.793 0.07489 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 5.289 on 162 degrees of freedom
## Multiple R-squared: 0.2097, Adjusted R-squared: 0.195
## F-statistic: 14.33 on 3 and 162 DF, p-value: 2.521e-08model2 <- lm(points ~ attitude, data = learning2014_readback)
summary(model2)##
## Call:
## lm(formula = points ~ attitude, data = learning2014_readback)
##
## Residuals:
## Min 1Q Median 3Q Max
## -16.9763 -3.2119 0.4339 4.1534 10.6645
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 11.6372 1.8303 6.358 1.95e-09 ***
## attitude 3.5255 0.5674 6.214 4.12e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 5.32 on 164 degrees of freedom
## Multiple R-squared: 0.1906, Adjusted R-squared: 0.1856
## F-statistic: 38.61 on 1 and 164 DF, p-value: 4.119e-09# Testing whether the model meets the assumptions of a linear regression
par(mfrow = c(2,2))
plot(model2, which = c(1,2,5))
date()## [1] "Mon Nov 20 15:47:17 2023"
Here we go again…
Assignment 3
Anne Tyvijärvi
This data includes information on student alcohol consumption, personal identifiers (age, sex, etc.), information about the family (education of parents, family size, etc.) and variables measuring the student’s success in school.
## [1] "school" "sex" "age" "address" "famsize"
## [6] "Pstatus" "Medu" "Fedu" "Mjob" "Fjob"
## [11] "reason" "guardian" "traveltime" "studytime" "schoolsup"
## [16] "famsup" "activities" "nursery" "higher" "internet"
## [21] "romantic" "famrel" "freetime" "goout" "Dalc"
## [26] "Walc" "health" "failures" "paid" "absences"
## [31] "G1" "G2" "G3" "alc_use" "high_use"I decided to study the relationships between low/high alcohol consumption and parental education (“Medu” for mother’s education and “Fedu” for father’s education), student’s current health status (“health”) and quality of family relationships (“famrel”).
I hypothesize that
- low level of education of either parent is associated with higher alcohol consumption in students
- the health status of a student is associated with higher alcohol consumption
- frequent alcohol use is associated with the quality of the relationship with the family
The mean age of the students was 16.6 years. The mean score for alcohol consumption (on a scale of 1 to 5, where 1 = very low consumption and 5 = very high consumption) was 1.9, indicating a moderate level of alcohol consumption across the data set. The mean scores for the education levels of the students mother and father were 2.8 and 2.6, indicating a slightly higher level of education for the mothers compared to fathers. Over all, the students health levels were really good (mean score 3.6), and in addition, the quality of the family relationships was really good (mean score of 3.9). The count summaries support the above findings.
## [1] 16.6## [1] 1.9## [1] 2.8## [1] 2.6## [1] 3.6## [1] 3.9## # A tibble: 7 × 2
## age count
## <dbl> <int>
## 1 15 81
## 2 16 102
## 3 17 97
## 4 18 77
## 5 19 11
## 6 20 1
## 7 22 1## # A tibble: 9 × 2
## alc_use count
## <dbl> <int>
## 1 1 140
## 2 1.5 63
## 3 2 56
## 4 2.5 41
## 5 3 32
## 6 3.5 17
## 7 4 9
## 8 4.5 3
## 9 5 9## # A tibble: 5 × 2
## Medu count
## <dbl> <int>
## 1 0 3
## 2 1 49
## 3 2 96
## 4 3 93
## 5 4 129## # A tibble: 5 × 2
## Fedu count
## <dbl> <int>
## 1 0 2
## 2 1 73
## 3 2 105
## 4 3 97
## 5 4 93## # A tibble: 5 × 2
## health count
## <dbl> <int>
## 1 1 46
## 2 2 42
## 3 3 80
## 4 4 62
## 5 5 140## # A tibble: 5 × 2
## famrel count
## <dbl> <int>
## 1 1 8
## 2 2 18
## 3 3 64
## 4 4 180
## 5 5 100Below, the charts show that in general, alcohol use seemed to be more frequent where either parent had a higher education. This is opposite to my first hypothesis.
In addition, in contrast to my second and third hypotheses, either poor health score or poor family relationships did not seem to be associated with more frequent alcohol use.
Now, let’s see if there are statistically significant differences associated with the variables that I’ve chosen and high alcohol use. Let’s set the “family = binomial” to let R know that the dependent variable high_use is binary (TRUE/FALSE).
Summary of the model shows a significant (p < 0.05 ) relationship between the quality of family relationships and high alcohol use. In addition, there is a trend of the health score being associated with high alcohol use (p < 0.1).
##
## Call:
## glm(formula = high_use ~ Medu + Fedu + health + famrel, family = "binomial",
## data = alc)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.18242 0.63354 -0.288 0.7734
## Medu -0.01537 0.13745 -0.112 0.9110
## Fedu 0.02092 0.13709 0.153 0.8787
## health 0.14777 0.08482 1.742 0.0815 .
## famrel -0.31087 0.12454 -2.496 0.0126 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 452.04 on 369 degrees of freedom
## Residual deviance: 443.49 on 365 degrees of freedom
## AIC: 453.49
##
## Number of Fisher Scoring iterations: 4## (Intercept) Medu Fedu health famrel
## -0.18242217 -0.01536970 0.02092328 0.14777237 -0.31086747Since the education of either parent does not explain high alcohol use, let’s remove them from the model see and see how that looks. Let’s also look at the coefficients/odd ratios and provide confidence intervals for them.
The summary shows a small increase/improvement in the p - value for “health”. From the coefficients and confidence interval output we can see that the odds of variable “health” is ~1.16, meaning that exposure to “high_use” was associated with higher odds of outcome for health. For family relationships (famrel), the odd ratio was 0.7 meaning that the exposure to “high_use” was associated with lower odds of outcome for the quality of family relationships. Around 30% of the variance in “health odd ratio” can be explained with 97,5% confidence interval (which is OK?), but for famrel the value is below zero (which is not good, I assume :D)
##
## Call:
## glm(formula = high_use ~ health + famrel, family = "binomial",
## data = alc)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.17461 0.54626 -0.320 0.7492
## health 0.14850 0.08465 1.754 0.0794 .
## famrel -0.31083 0.12454 -2.496 0.0126 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 452.04 on 369 degrees of freedom
## Residual deviance: 443.51 on 367 degrees of freedom
## AIC: 449.51
##
## Number of Fisher Scoring iterations: 4## odd_ratios 2.5 % 97.5 %
## (Intercept) 0.8397865 -1.25837614 0.89223235
## health 1.1600907 -0.01507081 0.31752786
## famrel 0.7328380 -0.55725045 -0.06718336Next, let’s explore the predictive power of our model glm2. The prediction got 256 (out of possible 259) FALSE observations “right”, so here the prediction works quite efficiently. However, when it comes to TRUE observations in the data, the prediction was not able to predict any of them (so the “result” is 0/111, which to me, sounds bad). Since I’m not a data scientist and this is my first time performing such analysis, I’m not quite sure how to interpret this. I’m sure (?) something in our model is not as is should be (I know at least that the variables health and famrel are not anywhere near normally distributed, so maybe that is one thing..?). The average number of incorrect predictions with probability 0 was 0.3, and with probability 1 it was 0.7.This means that when we have a binary (TRUE/FALSE and “positive”/“negative”) problem, any prediction that is set with the probability of 0 is the prediction for “FALSE” or “negative” => in our case, the average number of incorrect predictions for “FALSE” is 0.3, where as for “TRUE” it is 0.7. This was also reflected in the cross tabulation where the prediction failed with all TRUE predictions.
## prediction
## high_use FALSE TRUE
## FALSE 256 3
## TRUE 111 0## [1] 0.3## [1] 0.7Regarding the three hypothesis set in the beginning, it looked like student health and the quality of family relationships were associated with alcohol use, so my last two hypothese were confirmed. However, I found no support for the first hypothesis, and it looks like the education level of either parent is not associated with alcohol consumption in students.Based on the odd ratios and predictions my glm model did not really work well, but the time allocated for these exercises did not allow me to further explore what was “wrong” with it.
As final words I would like to declare that I put a lot of time and effort in these exercises, and although I might have not interpreted the results “correctly” and made a few mistakes, I really tried my best and gave it a 100 % effort. :) I hope you (whoever grades this) appreciate the effort I made (being new to all these things shows…) :)